NCGOCR

• Named Concept Gene Ontology Concept Recognition
• Automatic recognize Gene Ontology (GO) concepts from context.

Installation

Using 'pip' to install the Python module

$ pip install -U ncgocr

Usage

from ncgocr import Craft, GoData, NCGOCR, Corpus, evaluate

craft = Craft('data')
corpus = craft.get_corpus()
goldstandard = craft.get_goldstandard()

print('Loading GO...')
godata = GoData('data/craft-1.0/ontologies/GO.obo')

print('Initiating NCGOCR...')
ncgocr = NCGOCR(godata)

print('Training the model...')
ncgocr.train(corpus, goldstandard)

print('Loading the testing corpus...')
corpus_name = 'testing corpus'
testing_corpus = Corpus.from_dir('data/craft-1.0/articles/txt/', corpus_name)

print('predicting the results...')
result = ncgocr.process(testing_corpus)

print('Show the first 10 results...')
print(result.to_list()[:10])

print('Evaluate the results...')
report = evaluate(result, goldstandard, 'Using the training corpus as the testing corpus')
print(report)

License

• Free software: MIT license